Command line usage
------------------

Once the installation is successful, options for the corresponding usecase could be obtained by typing the corresponding command, or by adding ``-h`` flag to it:

 - ``visualqc_alignment``
 - ``visualqc_freesurfer``
 - ``visualqc_func_mri``
 - ``visualqc_anatomical``
 - ``visualqc_defacing``
 - ``visualqc_diffusion``

Each of them has a shorter name shortcut too to save a bit of typing :):

 - ``vqcalign``
 - ``vqcfs``
 - ``vqcfunc``
 - ``vqcanat``
 - ``vqcdeface``
 - ``vqcdwi``


For example,

.. code-block:: bash

    vqcalign
    vqcfunc -h


Those options for each command are shown in their respective pages:

 - :doc:`cli_alignment`
 - :doc:`cli_freesurfer`
 - :doc:`cli_func_mri`
 - :doc:`cli_defacing`
 - :doc:`cli_t1_mri`
 - :doc:`cli_diff_mri`


Check the bottom of this page for examples.


Examples showing the usage of each of these use cases are shown below:

 - :doc:`examples_freesurfer`
 - :doc:`examples_freesurfer_generic`
 - :doc:`examples_func_mri`
 - :doc:`examples_defacing`
 - :doc:`examples_alignment`
 - :doc:`examples_t1_mri`
 - :doc:`examples_diff_mri`